-/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
-package jalview.datamodel;\r
-\r
-import java.util.*;\r
-\r
-\r
-/** Data structure to hold and manipulate a multiple sequence alignment\r
- */\r
-public interface AlignmentI\r
-{\r
- /**\r
- * Calculates the number of sequences in an alignment\r
- *\r
- * @return Number of sequences in alignment\r
- */\r
- public int getHeight();\r
-\r
- /**\r
- * Calculates the maximum width of the alignment, including gaps.\r
- *\r
- * @return Greatest sequence length within alignment.\r
- */\r
- public int getWidth();\r
-\r
- /**\r
- * Calculates the longest sequence Id of the alignment\r
- *\r
- * @return Number of characters in longest sequence Id.\r
- */\r
- public int getMaxIdLength();\r
-\r
- /**\r
- * Calculates if this set of sequences is all the same length\r
- *\r
- * @return true if all sequences in alignment are the same length\r
- */\r
- public boolean isAligned();\r
-\r
- /**\r
- * Gets sequences as a Vector\r
- *\r
- * @return All sequences in alignment.\r
- */\r
- public Vector getSequences();\r
-\r
- /**\r
- * Find a specific sequence in this alignment.\r
- *\r
- * @param i Index of required sequence.\r
- *\r
- * @return SequenceI at given index.\r
- */\r
- public SequenceI getSequenceAt(int i);\r
-\r
- /**\r
- * Add a new sequence to this alignment.\r
- *\r
- * @param seq New sequence will be added at end of alignment.\r
- */\r
- public void addSequence(SequenceI seq);\r
-\r
- /**\r
- * Used to set a particular index of the alignment with the given sequence.\r
- *\r
- * @param i Index of sequence to be updated.\r
- * @param seq New sequence to be inserted.\r
- */\r
- public void setSequenceAt(int i, SequenceI seq);\r
-\r
- /**\r
- * Deletes a sequence from the alignment.\r
- *\r
- * @param s Sequence to be deleted.\r
- */\r
- public void deleteSequence(SequenceI s);\r
-\r
- /**\r
- * Deletes a sequence from the alignment.\r
- *\r
- * @param i Index of sequence to be deleted.\r
- */\r
- public void deleteSequence(int i);\r
-\r
- /**\r
- * Deletes all residues in every sequence of alignment within given columns.\r
- *\r
- * @param start Start index of columns to delete.\r
- * @param end End index to columns to delete.\r
- */\r
- public void deleteColumns(int start, int end);\r
-\r
- /**\r
- * Deletes all residues in every sequence of alignment within given columns.\r
- *\r
- * @param seq1 Index of first sequence to delete columns from.\r
- * @param seq2 Index of last sequence to delete columns from.\r
- * @param start Start index of columns to delete.\r
- * @param end End index of columns to delete.\r
- */\r
- public void deleteColumns(int seq1, int seq2, int start, int end);\r
-\r
- /**\r
- * Finds sequence in alignment using sequence name as query.\r
- *\r
- * @param name Id of sequence to search for.\r
- *\r
- * @return Sequence matching query, if found. If not found returns null.\r
- */\r
- public SequenceI findName(String name);\r
-\r
- /**\r
- * Finds sequence in alignment using full displayId as query.\r
- *\r
- * @param name displayId, ie <em>NAME/25-100</em>\r
- *\r
- * @return Sequence matching query, if found. If not found returns null.\r
- */\r
- public SequenceI findbyDisplayId(String name);\r
-\r
- /**\r
- * Finds index of a given sequence in the alignment.\r
- *\r
- * @param s Sequence to look for.\r
- *\r
- * @return Index of sequence within the alignment.\r
- */\r
- public int findIndex(SequenceI s);\r
-\r
- /**\r
- * All sequences will be cut from beginning to given index.\r
- *\r
- * @param i Remove all residues in sequences up to this column.\r
- */\r
- public void trimLeft(int i);\r
-\r
- /**\r
- * All sequences will be cut from given index.\r
- *\r
- * @param i Remove all residues in sequences beyond this column.\r
- */\r
- public void trimRight(int i);\r
-\r
- /**\r
- * Removes all columns containing entirely gap characters.\r
- */\r
- public void removeGaps();\r
-\r
- /**\r
- * Removes redundant sequences from alignment.\r
- *\r
- * @param threshold Remove all sequences above the given threshold.\r
- * @param sel Set of sequences which will have redundant sequences removed from.\r
- *\r
- * @return All sequences below redundancy threshold.\r
- */\r
- public Vector removeRedundancy(float threshold, Vector sel);\r
-\r
- /**\r
- * Finds group that sequence at index i in alignment is part of.\r
- *\r
- * @param i Index in alignment.\r
- *\r
- * @return First group found for sequence at position i. WARNING :\r
- * Sequences may be members of several groups. This method is incomplete.\r
- */\r
- public SequenceGroup findGroup(int i);\r
-\r
- /**\r
- * Finds group that given sequence is part of.\r
- *\r
- * @param s Sequence in alignment.\r
- *\r
- * @return First group found for sequence. WARNING :\r
- * Sequences may be members of several groups. This method is incomplete.\r
- */\r
- public SequenceGroup findGroup(SequenceI s);\r
-\r
- /**\r
- * Finds all groups that a given sequence is part of.\r
- *\r
- * @param s Sequence in alignment.\r
- *\r
- * @return All groups containing given sequence.\r
- */\r
- public SequenceGroup[] findAllGroups(SequenceI s);\r
-\r
- /**\r
- * Adds a new SequenceGroup to this alignment.\r
- *\r
- * @param sg New group to be added.\r
- */\r
- public void addGroup(SequenceGroup sg);\r
-\r
- /**\r
- * Deletes a specific SequenceGroup\r
- *\r
- * @param g Group will be deleted from alignment.\r
- */\r
- public void deleteGroup(SequenceGroup g);\r
-\r
- /**\r
- * Get all the groups associated with this alignment.\r
- *\r
- * @return All groups as a Vector.\r
- */\r
- public Vector getGroups();\r
-\r
- /**\r
- * Deletes all groups from this alignment.\r
- */\r
- public void deleteAllGroups();\r
-\r
- /**\r
- * Adds a super group. A SuperGroup is a group of groups.\r
- *\r
- * @param sg Adds a new SuperGroup to alignment\r
- */\r
- public void addSuperGroup(SuperGroup sg);\r
-\r
- /**\r
- * Removes SuperGroup from alignment.\r
- *\r
- * @param sg This SuperGroup will be deleted from alignment.\r
- */\r
- public void removeSuperGroup(SuperGroup sg);\r
-\r
- /**\r
- * Finds any SuperGroup that a given SequenceGroup may be part of.\r
- *\r
- * @param sg SequenceGroup to search for.\r
- *\r
- * @return SuperGroup that contains the given SequenceGroup.\r
- */\r
- public SuperGroup getSuperGroup(SequenceGroup sg);\r
-\r
- /**\r
- * Adds a new AlignmentAnnotation to this alignment\r
- */\r
- public void addAnnotation(AlignmentAnnotation aa);\r
-\r
- /**\r
- * Deletes a specific AlignmentAnnotation from the alignment.\r
- *\r
- * @param aa DOCUMENT ME!\r
- */\r
- public void deleteAnnotation(AlignmentAnnotation aa);\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public AlignmentAnnotation[] getAlignmentAnnotation();\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param gc DOCUMENT ME!\r
- */\r
- public void setGapCharacter(char gc);\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public char getGapCharacter();\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public Vector getAAFrequency();\r
-\r
- /**\r
- * Returns true if alignment is nucleotide sequence\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public boolean isNucleotide();\r
-\r
- /**\r
- * Set true if the alignment is a nucleotide sequence\r
- *\r
- * @return\r
- */\r
- public void setNucleotide(boolean b);\r
-\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General License for more details.
+ *
+ * You should have received a copy of the GNU General License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.datamodel;
+
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+/**
+ * Data structure to hold and manipulate a multiple sequence alignment
+ */
+public interface AlignmentI extends AnnotatedCollectionI
+{
+ /**
+ * Calculates the number of sequences in an alignment
+ *
+ * @return Number of sequences in alignment
+ */
+ int getHeight();
+
+ /**
+ *
+ * Calculates the maximum width of the alignment, including gaps.
+ *
+ * @return Greatest sequence length within alignment.
+ */
+ @Override
+ int getWidth();
+
+ /**
+ * Calculates if this set of sequences (visible and invisible) are all the
+ * same length
+ *
+ * @return true if all sequences in alignment are the same length
+ */
+ boolean isAligned();
+
+ /**
+ * Calculates if this set of sequences is all the same length
+ *
+ * @param includeHidden
+ * optionally exclude hidden sequences from test
+ * @return true if all (or just visible) sequences are the same length
+ */
+ boolean isAligned(boolean includeHidden);
+
+ /**
+ * Gets sequences as a Synchronized collection
+ *
+ * @return All sequences in alignment.
+ */
+ @Override
+ List<SequenceI> getSequences();
+
+ /**
+ * Gets sequences as a SequenceI[]
+ *
+ * @return All sequences in alignment.
+ */
+ SequenceI[] getSequencesArray();
+
+ /**
+ * Find a specific sequence in this alignment.
+ *
+ * @param i
+ * Index of required sequence.
+ *
+ * @return SequenceI at given index.
+ */
+ SequenceI getSequenceAt(int i);
+
+ /**
+ * Returns a map of lists of sequences keyed by sequence name.
+ *
+ * @return
+ */
+ Map<String, List<SequenceI>> getSequencesByName();
+
+ /**
+ * Add a new sequence to this alignment.
+ *
+ * @param seq
+ * New sequence will be added at end of alignment.
+ */
+ void addSequence(SequenceI seq);
+
+ /**
+ * Used to set a particular index of the alignment with the given sequence.
+ *
+ * @param i
+ * Index of sequence to be updated.
+ * @param seq
+ * New sequence to be inserted.
+ */
+ void setSequenceAt(int i, SequenceI seq);
+
+ /**
+ * Deletes a sequence from the alignment
+ *
+ * @param s
+ * Sequence to be deleted.
+ */
+ void deleteSequence(SequenceI s);
+
+ /**
+ * Deletes a sequence from the alignment.
+ *
+ * @param i
+ * Index of sequence to be deleted.
+ */
+ void deleteSequence(int i);
+
+ /**
+ * Finds sequence in alignment using sequence name as query.
+ *
+ * @param name
+ * Id of sequence to search for.
+ *
+ * @return Sequence matching query, if found. If not found returns null.
+ */
+ SequenceI findName(String name);
+
+ SequenceI[] findSequenceMatch(String name);
+
+ /**
+ * Finds index of a given sequence in the alignment.
+ *
+ * @param s
+ * Sequence to look for.
+ *
+ * @return Index of sequence within the alignment or -1 if not found
+ */
+ int findIndex(SequenceI s);
+
+ /**
+ * Finds group that given sequence is part of.
+ *
+ * @param s
+ * Sequence in alignment.
+ *
+ * @return First group found for sequence. WARNING : Sequences may be members
+ * of several groups. This method is incomplete.
+ */
+ SequenceGroup findGroup(SequenceI s);
+
+ /**
+ * Finds all groups that a given sequence is part of.
+ *
+ * @param s
+ * Sequence in alignment.
+ *
+ * @return All groups containing given sequence.
+ */
+ SequenceGroup[] findAllGroups(SequenceI s);
+
+ /**
+ * Adds a new SequenceGroup to this alignment.
+ *
+ * @param sg
+ * New group to be added.
+ */
+ void addGroup(SequenceGroup sg);
+
+ /**
+ * Deletes a specific SequenceGroup
+ *
+ * @param g
+ * Group will be deleted from alignment.
+ */
+ void deleteGroup(SequenceGroup g);
+
+ /**
+ * Get all the groups associated with this alignment.
+ *
+ * @return All groups as a list.
+ */
+ List<SequenceGroup> getGroups();
+
+ /**
+ * Deletes all groups from this alignment.
+ */
+ void deleteAllGroups();
+
+ /**
+ * Adds a new AlignmentAnnotation to this alignment
+ *
+ * @note Care should be taken to ensure that annotation is at least as wide as
+ * the longest sequence in the alignment for rendering purposes.
+ */
+ void addAnnotation(AlignmentAnnotation aa);
+
+ /**
+ * moves annotation to a specified index in alignment annotation display stack
+ *
+ * @param aa
+ * the annotation object to be moved
+ * @param index
+ * the destination position
+ */
+ void setAnnotationIndex(AlignmentAnnotation aa, int index);
+
+ /**
+ * Delete all annotations, including auto-calculated if the flag is set true.
+ * Returns true if at least one annotation was deleted, else false.
+ *
+ * @param includingAutoCalculated
+ * @return
+ */
+ boolean deleteAllAnnotations(boolean includingAutoCalculated);
+
+ /**
+ * Deletes a specific AlignmentAnnotation from the alignment, and removes its
+ * reference from any SequenceI or SequenceGroup object's annotation if and
+ * only if aa is contained within the alignment's annotation vector.
+ * Otherwise, it will do nothing.
+ *
+ * @param aa
+ * the annotation to delete
+ * @return true if annotation was deleted from this alignment.
+ */
+ boolean deleteAnnotation(AlignmentAnnotation aa);
+
+ /**
+ * Deletes a specific AlignmentAnnotation from the alignment, and optionally
+ * removes any reference from any SequenceI or SequenceGroup object's
+ * annotation if and only if aa is contained within the alignment's annotation
+ * vector. Otherwise, it will do nothing.
+ *
+ * @param aa
+ * the annotation to delete
+ * @param unhook
+ * flag indicating if any references should be removed from
+ * annotation - use this if you intend to add the annotation back
+ * into the alignment
+ * @return true if annotation was deleted from this alignment.
+ */
+ boolean deleteAnnotation(AlignmentAnnotation aa, boolean unhook);
+
+ /**
+ * Get the annotation associated with this alignment (this can be null if no
+ * annotation has ever been created on the alignment)
+ *
+ * @return array of AlignmentAnnotation objects
+ */
+ @Override
+ AlignmentAnnotation[] getAlignmentAnnotation();
+
+ /**
+ * Change the gap character used in this alignment to 'gc'
+ *
+ * @param gc
+ * the new gap character.
+ */
+ void setGapCharacter(char gc);
+
+ /**
+ * Get the gap character used in this alignment
+ *
+ * @return gap character
+ */
+ char getGapCharacter();
+
+ /**
+ * Test for all nucleotide alignment
+ *
+ * @return true if alignment is nucleotide sequence
+ */
+ boolean isNucleotide();
+
+ /**
+ * Test if alignment contains RNA structure
+ *
+ * @return true if RNA structure AligmnentAnnotation was added to alignment
+ */
+ boolean hasRNAStructure();
+
+ /**
+ * Set alignment to be a nucleotide sequence
+ *
+ */
+ void setNucleotide(boolean b);
+
+ /**
+ * Get the associated dataset for the alignment.
+ *
+ * @return Alignment containing dataset sequences or null of this is a
+ * dataset.
+ */
+ Alignment getDataset();
+
+ /**
+ * Set the associated dataset for the alignment, or create one.
+ *
+ * @param dataset
+ * The dataset alignment or null to construct one.
+ */
+ void setDataset(Alignment dataset);
+
+ /**
+ * pads sequences with gaps (to ensure the set looks like an alignment)
+ *
+ * @return boolean true if alignment was modified
+ */
+ boolean padGaps();
+
+ HiddenSequences getHiddenSequences();
+
+ /**
+ * Compact representation of alignment
+ *
+ * @return CigarArray
+ */
+ CigarArray getCompactAlignment();
+
+ /**
+ * Set an arbitrary key value pair for an alignment. Note: both key and value
+ * objects should return a meaningful, human readable response to .toString()
+ *
+ * @param key
+ * @param value
+ */
+ void setProperty(Object key, Object value);
+
+ /**
+ * Get a named property from the alignment.
+ *
+ * @param key
+ * @return value of property
+ */
+ Object getProperty(Object key);
+
+ /**
+ * Get the property hashtable.
+ *
+ * @return hashtable of alignment properties (or null if none are defined)
+ */
+ Hashtable getProperties();
+
+ /**
+ * add a reference to a frame of aligned codons for this alignment
+ *
+ * @param codons
+ */
+ void addCodonFrame(AlignedCodonFrame codons);
+
+ /**
+ * remove a particular codon frame reference from this alignment
+ *
+ * @param codons
+ * @return true if codon frame was removed.
+ */
+ boolean removeCodonFrame(AlignedCodonFrame codons);
+
+ /**
+ * get all codon frames associated with this alignment
+ *
+ * @return
+ */
+ Set<AlignedCodonFrame> getCodonFrames();
+
+ /**
+ * Set the codon frame mappings (replacing any existing set).
+ */
+ void setCodonFrames(Set<AlignedCodonFrame> acfs);
+
+ /**
+ * get codon frames involving sequenceI
+ */
+ List<AlignedCodonFrame> getCodonFrame(SequenceI seq);
+
+ /**
+ * find sequence with given name in alignment
+ *
+ * @param token
+ * name to find
+ * @param b
+ * true implies that case insensitive matching will <em>also</em> be
+ * tried
+ * @return matched sequence or null
+ */
+ SequenceI findName(String token, boolean b);
+
+ /**
+ * find next sequence with given name in alignment starting after a given
+ * sequence
+ *
+ * @param startAfter
+ * the sequence after which the search will be started (usually the
+ * result of the last call to findName)
+ * @param token
+ * name to find
+ * @param b
+ * true implies that case insensitive matching will <em>also</em> be
+ * tried
+ * @return matched sequence or null
+ */
+ SequenceI findName(SequenceI startAfter, String token, boolean b);
+
+ /**
+ * find first sequence in alignment which is involved in the given search
+ * result object
+ *
+ * @param results
+ * @return -1 or index of sequence in alignment
+ */
+ int findIndex(SearchResults results);
+
+ /**
+ * append sequences and annotation from another alignment object to this one.
+ * Note: this is a straight transfer of object references, and may result in
+ * toappend's dependent data being transformed to fit the alignment (changing
+ * gap characters, etc...). If you are uncertain, use the copy Alignment copy
+ * constructor to create a new version which can be appended without side
+ * effect.
+ *
+ * @param toappend
+ * - the alignment to be appended.
+ */
+ void append(AlignmentI toappend);
+
+ /**
+ * Justify the sequences to the left or right by deleting and inserting gaps
+ * before the initial residue or after the terminal residue
+ *
+ * @param right
+ * true if alignment padded to right, false to justify to left
+ * @return true if alignment was changed TODO: return undo object
+ */
+ boolean justify(boolean right);
+
+ /**
+ * add given annotation row at given position (0 is start, -1 is end)
+ *
+ * @param consensus
+ * @param i
+ */
+ void addAnnotation(AlignmentAnnotation consensus, int i);
+
+ /**
+ * search for or create a specific annotation row on the alignment
+ *
+ * @param name
+ * name for annotation (must match)
+ * @param calcId
+ * calcId for the annotation (null or must match)
+ * @param autoCalc
+ * - value of autocalc flag for the annotation
+ * @param seqRef
+ * - null or specific sequence reference
+ * @param groupRef
+ * - null or specific group reference
+ * @param method
+ * - CalcId for the annotation (must match)
+ *
+ * @return existing annotation matching the given attributes
+ */
+ AlignmentAnnotation findOrCreateAnnotation(String name, String calcId,
+ boolean autoCalc, SequenceI seqRef, SequenceGroup groupRef);
+
+ /**
+ * move the given group up or down in the alignment by the given number of
+ * rows. Implementor assumes given group is already present on alignment - no
+ * recalculations are triggered.
+ *
+ * @param sg
+ * @param map
+ * @param up
+ * @param i
+ */
+ void moveSelectedSequencesByOne(SequenceGroup sg,
+ Map<SequenceI, SequenceCollectionI> map, boolean up);
+
+ /**
+ * validate annotation after an edit and update any alignment state flags
+ * accordingly
+ *
+ * @param alignmentAnnotation
+ */
+ void validateAnnotation(AlignmentAnnotation alignmentAnnotation);
+
+ /**
+ * Align this alignment the same as the given one. If both of the same type
+ * (nucleotide/protein) then align both identically. If this is nucleotide and
+ * the other is protein, make 3 gaps for each gap in the protein sequences. If
+ * this is protein and the other is nucleotide, insert a gap for each 3 gaps
+ * (or part thereof) between nucleotide bases. Returns the number of mapped
+ * sequences that were realigned .
+ *
+ * @param al
+ * @return
+ */
+ int alignAs(AlignmentI al);
+
+ /**
+ * Returns the set of distinct sequence names in the alignment.
+ *
+ * @return
+ */
+ Set<String> getSequenceNames();
+
+ /**
+ * Checks if the alignment has at least one sequence with one non-gaped
+ * residue
+ *
+ * @return
+ */
+ public boolean hasValidSequence();
+}
git://source.jalview.org / jalview.git / blobdiff